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3. Network Visualization using Cytoscape

Step 1: Download Cytoscape to your Laptop

Step 2: Download Smoothie Outputs to your Laptop

  1. The function smoothie.make_spatal_network saves output files network_[...].csv and nodelabels_[...].csv. Download these two files from your server to your local laptop with Cytoscape installed.
  2. Additionally, download smoothie_cytoscape_colors.xml from the Smoothie Github https://github.com/caholdener01/Smoothie/blob/main/smoothie_cytoscape_colors.xml.

Step 3: Import Files into Cytoscape

  1. File > Import > Network From File...: Select network_[...].csv from your laptop.
  2. File > Import > Table From File...: Select nodelabels_[...].csv from your laptop.

  3. File > Import > Styles From File... Select smoothie_cytoscape_colors.xml from your laptop.

    import_files_to_cytoscape.png

Step 4: Configure Network Styles

  1. Change your current default style to the new smoothie_cytoscape_colors style we just imported.

    change_styles_pt1.png change_styles_pt2.png

  2. The network nodes should be colored by module label now. You may adjust other network stylistic features within the styles tab too.

    colorful_network.png

(Optional) Step 5: Tidy up the Network's Appearance

  1. Add an edge filter for the network (Use the PCC column).

    network_tidying_pt1.png network_tidying_pt2.png

  2. Slightly increase the PCC lower filter value (by 0.05 to 0.1) and apply the filter.

    network_tidying_pt3.png

  3. Next, select nodes connected by selected edges, and hide non-selected nodes and edges.

    network_tidying_pt4.png network_tidying_pt5.png

  4. Export the network.

    network_tidying_pt6.png network_tidying_pt7.png

(Optional) Step 6: Explore Network Further

Cytoscape has many useful features. You can create different node/edge filters or explore more built-in features here: https://cytoscape.org/.